Joining objects good practices?
Joining this way, especially facial work, probably won't serve you well in the long run.  The biggest issue you face, which you have already picked up on, is that it will disturb your topology.  Longer term, the layout of faces and vertices doing it this way won't serve facial animation if you ever want to do anything. Think about smiling, for example.  You would have to fight the direction of those edges to make it turn up.  And in some areas where you need more fine detail, like around the eyes, you won't have it.
For example, look at the meshes here....
https://cgcookie.com/course/mesh-modeling-bootcamp
You can see how the mesh serves the animation (see the face loop video).  Now in your case, it doesn't look like you have to do anything that complicated, but I would recommend following a tutorial like that one.  One, you will probably learn a lot of great new stuff and it will get you ready for what you may want in the future for this project.
Good luck!